Hii all I am trying to simulate biomolecule in Guanidinium chloride in AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in energy minimization step but in NVT step files are generated and shows segmentation fault(core dumped). How to solve this problem? I have verified the topology of GdmCl by matching the density with the experimental density. My another question is that should I proceed with the topology by matching density only? Looking for some suggestions.
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